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comparison test-data/test_1_output_log_file.contains @ 2:74c9214cc8e6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 4d5b98367b51a9e2f2711d1ccea9753a415d973a
author devteam
date Wed, 24 Oct 2018 11:31:03 -0400
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1:4a14714649b4 2:74c9214cc8e6
1 #############################################
2 ###### SICER v1.1 ######
3 #############################################
4 Input library directory:
5 ChIP library:
6 Output directory:
7 Species: mm8
8 Threshold for redundancy allowed for reads: 1
9 Window size: 200 bps
10 Fragment size: 150 bps. The shift for reads is half of 150
11 Effective genome size as a fraction of the reference genome of mm8: 0.740000
12 Gap size: 600 bps
13 Evalue for identification of significant islands: 0.01
14 Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
15 chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963
16 chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
17 chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
18 chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
19 chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
20 chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
21 chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
22 chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
23 chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
24 chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
25 chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
26 chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
27 chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
28 chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
29 chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
30 chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
31 chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
32 chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
33 chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
34 chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
35 chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
36 chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
37 Partion the genome in windows ...
38 Generate summary files for input_bed_file...
39 total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
40 total tag count in chr2.bed is: 0.0 = 0.0+0.0
41 total tag count in chr3.bed is: 0.0 = 0.0+0.0
42 total tag count in chr4.bed is: 0.0 = 0.0+0.0
43 total tag count in chr5.bed is: 0.0 = 0.0+0.0
44 total tag count in chr6.bed is: 0.0 = 0.0+0.0
45 total tag count in chr7.bed is: 0.0 = 0.0+0.0
46 total tag count in chr8.bed is: 0.0 = 0.0+0.0
47 total tag count in chr9.bed is: 0.0 = 0.0+0.0
48 total tag count in chr10.bed is: 0.0 = 0.0+0.0
49 total tag count in chr11.bed is: 0.0 = 0.0+0.0
50 total tag count in chr12.bed is: 0.0 = 0.0+0.0
51 total tag count in chr13.bed is: 0.0 = 0.0+0.0
52 total tag count in chr14.bed is: 0.0 = 0.0+0.0
53 total tag count in chr15.bed is: 0.0 = 0.0+0.0
54 total tag count in chr16.bed is: 0.0 = 0.0+0.0
55 total tag count in chr17.bed is: 0.0 = 0.0+0.0
56 total tag count in chr18.bed is: 0.0 = 0.0+0.0
57 total tag count in chr19.bed is: 0.0 = 0.0+0.0
58 total tag count in chrX.bed is: 0.0 = 0.0+0.0
59 total tag count in chrY.bed is: 0.0 = 0.0+0.0
60 total tag count in chrM.bed is: 0.0 = 0.0+0.0
61 Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...
62 Convert the normalized summary graph into wig vstep format...
63 Find significant islands with E-value 0.01 for input_bed_file...
64 Species: mm8
65 Window_size: 200
66 Gap size: 600
67 E value is: 0.01
68 Total read count: 9898.0
69 Genome Length: 2644093988
70 Effective genome Length: 1956629551
71 Window average: 0.0010117398048
72 Window pvalue: 0.2
73 Minimum num of tags in a qualified window: 1
74 Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows
75 Determine the score threshold from random background
76 The score threshold is: 21.384
77 Make and write islands
78 Total number of islands: 352
79 Filter reads with identified significant islands for input_bed_file...
80 Make summary graph with filtered reads for input_bed_file...
81 total tag count in chr1.bed is: 9654.0 = 4808.0+4846.0
82 total tag count in chr2.bed is: 0.0 = 0.0+0.0
83 total tag count in chr3.bed is: 0.0 = 0.0+0.0
84 total tag count in chr4.bed is: 0.0 = 0.0+0.0
85 total tag count in chr5.bed is: 0.0 = 0.0+0.0
86 total tag count in chr6.bed is: 0.0 = 0.0+0.0
87 total tag count in chr7.bed is: 0.0 = 0.0+0.0
88 total tag count in chr8.bed is: 0.0 = 0.0+0.0
89 total tag count in chr9.bed is: 0.0 = 0.0+0.0
90 total tag count in chr10.bed is: 0.0 = 0.0+0.0
91 total tag count in chr11.bed is: 0.0 = 0.0+0.0
92 total tag count in chr12.bed is: 0.0 = 0.0+0.0
93 total tag count in chr13.bed is: 0.0 = 0.0+0.0
94 total tag count in chr14.bed is: 0.0 = 0.0+0.0
95 total tag count in chr15.bed is: 0.0 = 0.0+0.0
96 total tag count in chr16.bed is: 0.0 = 0.0+0.0
97 total tag count in chr17.bed is: 0.0 = 0.0+0.0
98 total tag count in chr18.bed is: 0.0 = 0.0+0.0
99 total tag count in chr19.bed is: 0.0 = 0.0+0.0
100 total tag count in chrX.bed is: 0.0 = 0.0+0.0
101 total tag count in chrY.bed is: 0.0 = 0.0+0.0
102 total tag count in chrM.bed is: 0.0 = 0.0+0.0
103 Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
104 Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...
105 Done!
106 Additionally, these warnings were reported:
107 Warning: chr2 reads do not exist in
108 Warning: chr3 reads do not exist in
109 Warning: chr4 reads do not exist in
110 Warning: chr5 reads do not exist in
111 Warning: chr6 reads do not exist in
112 Warning: chr7 reads do not exist in
113 Warning: chr8 reads do not exist in
114 Warning: chr9 reads do not exist in
115 Warning: chr10 reads do not exist in
116 Warning: chr11 reads do not exist in
117 Warning: chr12 reads do not exist in
118 Warning: chr13 reads do not exist in
119 Warning: chr14 reads do not exist in
120 Warning: chr15 reads do not exist in
121 Warning: chr16 reads do not exist in
122 Warning: chr17 reads do not exist in
123 Warning: chr18 reads do not exist in
124 Warning: chr19 reads do not exist in
125 Warning: chrX reads do not exist in
126 Warning: chrY reads do not exist in
127 Warning: chrM reads do not exist in
128 Warning: chr2 reads do not exist in
129 Warning: chr3 reads do not exist in
130 Warning: chr4 reads do not exist in
131 Warning: chr5 reads do not exist in
132 Warning: chr6 reads do not exist in
133 Warning: chr7 reads do not exist in
134 Warning: chr8 reads do not exist in
135 Warning: chr9 reads do not exist in
136 Warning: chr10 reads do not exist in
137 Warning: chr11 reads do not exist in
138 Warning: chr12 reads do not exist in
139 Warning: chr13 reads do not exist in
140 Warning: chr14 reads do not exist in
141 Warning: chr15 reads do not exist in
142 Warning: chr16 reads do not exist in
143 Warning: chr17 reads do not exist in
144 Warning: chr18 reads do not exist in
145 Warning: chr19 reads do not exist in
146 Warning: chrX reads do not exist in
147 Warning: chrY reads do not exist in
148 Warning: chrM reads do not exist in
149 Warning: chr2 reads do not exist in
150 Warning: chr3 reads do not exist in
151 Warning: chr4 reads do not exist in
152 Warning: chr5 reads do not exist in
153 Warning: chr6 reads do not exist in
154 Warning: chr7 reads do not exist in
155 Warning: chr8 reads do not exist in
156 Warning: chr9 reads do not exist in
157 Warning: chr10 reads do not exist in
158 Warning: chr11 reads do not exist in
159 Warning: chr12 reads do not exist in
160 Warning: chr13 reads do not exist in
161 Warning: chr14 reads do not exist in
162 Warning: chr15 reads do not exist in
163 Warning: chr16 reads do not exist in
164 Warning: chr17 reads do not exist in
165 Warning: chr18 reads do not exist in
166 Warning: chr19 reads do not exist in
167 Warning: chrX reads do not exist in
168 Warning: chrY reads do not exist in
169 Warning: chrM reads do not exist in
170 Warning: chr2 reads do not exist in
171 Warning: chr3 reads do not exist in
172 Warning: chr4 reads do not exist in
173 Warning: chr5 reads do not exist in
174 Warning: chr6 reads do not exist in
175 Warning: chr7 reads do not exist in
176 Warning: chr8 reads do not exist in
177 Warning: chr9 reads do not exist in
178 Warning: chr10 reads do not exist in
179 Warning: chr11 reads do not exist in
180 Warning: chr12 reads do not exist in
181 Warning: chr13 reads do not exist in
182 Warning: chr14 reads do not exist in
183 Warning: chr15 reads do not exist in
184 Warning: chr16 reads do not exist in
185 Warning: chr17 reads do not exist in
186 Warning: chr18 reads do not exist in
187 Warning: chr19 reads do not exist in
188 Warning: chrX reads do not exist in
189 Warning: chrY reads do not exist in
190 Warning: chrM reads do not exist in